MADS-box gene family plays an important role in the development of floral organs in plants. A full-length cDNA of MADS-box gene, named as GbSEP(Genbank accession numberKJ630504), was cloned by RT-PCR from female flower of Ginkgo biloba. The cDNA sequence of GbSEP contained an ORF of 756 bp encoding 252 amino acid residues. The comparison between cDNA and genomic sequences of GbSEP indicated no intron in the genomic DNA sequence of this gene. Protein multi-alignment analysis indicated that GbSEP shared high homology with other SEP family proteins from other plants including Pinus radiate (PrMADS3), Pinus resinosa (PrMADS1), Arabidopsis thaliana (AtSEP4), Alpinia hainanensis (AhSEP3), Lotus japonicas (LjSEP), Populus tomentosa (PtSEP), and Mangifera indica (MiSEP3). Moreover, GbSEP contained a MADS-box and a K-box domain, typical conservative domains of plant MADS-box proteins. Phylogenetic tree clearly showed that GbSEP is classed into SEP subgroup of E class MADS-box protein family. Real-time PCR analysis revealed that expression levels of GbSEP gene in female and male flower were significantly higher than those in root, stem, and leaves, and that GbSEP expression level increased along with time of flower development, suggesting that GbSEP might be involved in development of reproductive organs in G. biloba.